Search Results - "AUDIT, B"

Revealing long-range interconnected hubs in human chromatin interaction data using graph theory by Boulos, R E, Arneodo, A, Jensen, P, Audit, B

“…We use graph theory to analyze chromatin interaction (Hi-C) data in the human genome. We show that a key functional feature of the genome--"master" replication…”
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SWDreader: A wavelet-based algorithm using spectral phase to characterize spike-wave morphological variation in genetic models of absence epilepsy by Richard, C.D., Tanenbaum, A., Audit, B., Arneodo, A., Khalil, A., Frankel, W.N.

“…•Standard terms of EEG/ECoG morphology are ill-suited to analyzing seizure variants.•Categorical descriptions are used because morphology eludes numerical…”
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Experiments confirm the influence of genome long-range correlations on nucleosome positioning by Vaillant, C, Audit, B, Arneodo, A

“…From the statistical analysis of nucleosome positioning data for chromosome III of S. cerevisiae, we demonstrate that long-range correlations (LRC) in the…”
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Deciphering DNA replication dynamics in eukaryotic cell populations in relation with their averaged chromatin conformations by Goldar, A., Arneodo, A., Audit, B., Argoul, F., Rappailles, A., Guilbaud, G., Petryk, N., Kahli, M., Hyrien, O.

“…We propose a non-local model of DNA replication that takes into account the observed uncertainty on the position and time of replication initiation in…”
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Inferring where and when replication initiates from genome-wide replication timing data by Baker, A, Audit, B, Yang, S C-H, Bechhoefer, J, Arneodo, A

“…Based on an analogy between DNA replication and one dimensional nucleation-and-growth processes, various attempts to infer the local initiation rate I(x,t) of…”
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Replication-Associated Strand Asymmetries in Mammalian Genomes: Toward Detection of Replication Origins by Touchon, Marie, Nicolay, Samuel, Audit, Benjamin, Edward-Benedict Brodie of Brodie, d'Aubenton-Carafa, Yves, Arneodo, Alain, Thermes, Claude, Green, Philip P.

“…In the course of evolution, mutations do not affect both strands of genomic DNA equally. This imbalance mainly results from asymmetric DNA mutation and repair…”
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Linking the DNA strand asymmetry to the spatio-temporal replication program: II. Accounting for neighbor-dependent substitution rates by Baker, A., Chen, C. L., Julienne, H., Audit, B., d’Aubenton-Carafa, Y., Thermes, C., Arneodo, A.

“…In paper I, we addressed the impact of the spatio-temporal program on the DNA composition evolution in the case of time homogeneous and neighbor-independent…”
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Linking the DNA strand asymmetry to the spatio-temporal replication program: I. About the role of the replication fork polarity in genome evolution by Baker, A., Julienne, H., Chen, C. L., Audit, B., d’Aubenton-Carafa, Y., Thermes, C., Arneodo, A.

“…Two key cellular processes, namely transcription and replication, require the opening of the DNA double helix and act differently on the two DNA strands,…”
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Revisiting polymer statistical physics to account for the presence of long-range-correlated structural disorder in 2D DNA chains by Moukhtar, J., Vaillant, C., Audit, B., Arneodo, A.

“…We elaborate on a generalization of the 2D wormlike chain (WLC) model that accounts for the presence of long-range correlations (LRC) in the intrinsic…”
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Long-range correlations in genomic DNA: a signature of the nucleosomal structure by Audit, B, Thermes, C, Vaillant, C, d'Aubenton-Carafa, Y, Muzy, J F, Arneodo, A

“…We use the "wavelet transform microscope" to carry out a comparative statistical analysis of DNA bending profiles and of the corresponding DNA texts. In the…”
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Revealing intermittency in experimental data with steep power spectra by Falcon, E, Roux, S. G, Audit, B

“…The statistics of signal increments are commonly used in order to test for possible intermittent properties in experimental or synthetic data. However, for…”
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Generalized wormlike chain model for long-range correlated heteropolymers by Moukhtar, J, Vaillant, C, Audit, B, Arneodo, A

“…We extend the 2D wormlike chain model (WLC) for semiflexible polymers to long-range correlated (LRC) heteropolymers. The conjugated contributions of i) the…”
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Thermodynamics of DNA loops with long-range correlated structural disorder by VAILLANT, C, AUDIT, B, AMEODO, A

“…We study the influence of a structural disorder on the thermodynamical properties of 2D-elastic chains submitted to mechanical/topological constraint as loops…”
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Wavelet-based estimators of scaling behavior by Audit, B., Bacry, E., Muzy, J.-F., Arneodo, A.

“…Various wavelet-based estimators of self-similarity or long-range dependence scaling exponent are studied extensively. These estimators mainly include the…”
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DNA replication timing data corroborate in silico human replication origin predictions by Audit, B, Nicolay, S, Huvet, M, Touchon, M, d'Aubenton-Carafa, Y, Thermes, C, Arneodo, A

“…We develop a wavelet-based multiscale pattern recognition methodology to disentangle the replication- from the transcription-associated compositional strand…”
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Spontaneous emergence of sequence-dependent rosettelike folding of chromatin fiber by St-Jean, Ph, Vaillant, C, Audit, B, Arneodo, A

“…In the crowded environment of the eukaryotic nucleus, the presence of intrinsic structural defects is shown to predispose chromatin fiber to spontaneously form…”
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From DNA sequence analysis to modeling replication in the human genome by BRODIE OF BRODIE, E. B, NICOLAY, S, TOUCHER, M, AUDIT, B, D'AUBENTON-CARAFA, Y, THERMES, C, AMEODO, A

“…We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication…”
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Formation and positioning of nucleosomes: effect of sequence-dependent long-range correlated structural disorder by Vaillant, C, Audit, B, Thermes, C, Arnéodo, A

“…The understanding of the long-range correlations (LRC) observed in DNA sequences is still an open and very challenging problem. In this paper, we start…”
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Strain-specific genes of Helicobacter pylori: distribution, function and dynamics by Janssen, P J, Audit, B, Ouzounis, C A

“…Whole-genome clustering of the two available genome sequences of Helicobacter pylori strains 26695 and J99 allows the detection of 110 and 52 strain-specific…”
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CoGenT++: an extensive and extensible data environment for computational genomics by Goldovsky, Leon, Janssen, Paul, Ahrén, Dag, Audit, Benjamin, Cases, Ildefonso, Darzentas, Nikos, Enright, Anton J., López-Bigas, Núria, Peregrin-Alvarez, José M., Smith, Mike, Tsoka, Sophia, Kunin, Victor, Ouzounis, Christos A.

“…Motivation: CoGenT++ is a data environment for computational research in comparative and functional genomics, designed to address issues of consistency,…”
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